I'm aware of the reason behind the clicking/popping noise but was I thought I had seen in some threads where the noise was more pronounced when using the L6 link via an HD POD to change the topologies rather than the faceplate switches. Is that true? If so does anyone have any ideas why that may be?

It's not true, unfortunately. Switching topologies on the amp itself or the HD is the same. You're just using the HD as digital control over the output stage of the amp. The reason for the noise is because the bias circuit voltages have to be changed in a major way, and the ramp up/down in voltage gets amplified. I just use amp models with the same topology within a song usually, or live with the pop/delay which probably can't be heard over our bashing drummer anyway!

The information above may not be current, and you should direct questions to the current forum or review the manual.